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This article is part of the supplement: Proceedings of the 12th European workshop on QTL mapping and marker assisted selection

Open Access Introduction

Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping

Lucy Crooks1, Goutam Sahana2, Dirk-Jan de Koning3, Mogens Sandø Lund2 and Örjan Carlborg1*

Author Affiliations

1 Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-75007 Uppsala, Sweden

2 University of Aarhus, Faculty of Agricultural Sciences, Department of Genetics & Biotechnology, Research Centre Foulum, DK-8830, Box 50, Tjele, Denmark

3 The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin Biocentre, Roslin, Midlothian, EH25 9PS, UK

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BMC Proceedings 2009, 3(Suppl 1):S2  doi:10.1186/1753-6561-3-S1-S2

Published: 23 February 2009


As part of the QTLMAS XII workshop, a simulated dataset was distributed and participants were invited to submit analyses of the data based on genome-wide association, fine mapping and genomic selection. We have evaluated the findings from the groups that reported fine mapping and genome-wide association (GWA) efforts to map quantitative trait loci (QTL). Generally the power to detect QTL was high and the Type 1 error was low. Estimates of QTL locations were generally very accurate. Some methods were much better than others at estimating QTL effects, and with some the accuracy depended on simulated effect size or minor allele frequency. There were also indications of bias in the effect estimates. No epistasis was simulated, but the two studies that included searches for epistasis reported several interacting loci, indicating a problem with controlling the Type I error rate in these analyses. Although this study is based on a single dataset, it indicates that there is a need to improve fine mapping and GWA methods with respect to estimation of genetic effects, appropriate choice of significance thresholds and analysis of epistasis.